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add horizontal crop
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@rthiermann
rthiermann committed Sep 19, 2023
1 parent 272b3c9 commit 4809c96
Showing 1 changed file with 54 additions and 17 deletions.
71 changes: 54 additions & 17 deletions src/napari_mm3/_tiff_converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -129,10 +129,11 @@ def bioformats_import(
image_start: int,
image_end: int,
vertical_crop=None,
horizontal_crop=None,
tworow_crop=None,
fov_list=[],
):
""" Imports a bioformats-compatible file into a tif stack.
"""Imports a bioformats-compatible file into a tif stack.
Parameters
----------
data_path : Path
Expand All @@ -146,7 +147,9 @@ def bioformats_import(
vertical_crop : tuple, optional
The vertical crop to apply to the image. The default is None.
tworow_crop : tuple, optional
The two-row crop to apply to the image. The default is None.
The two-row (vertical) crop to apply to the image. The default is None.
horizontal_crop: tuple, optional
The horizontal crop to apply to the image. The default is None.
fov_list : list, optional
The list of fovs to import. The default is [].
Returns
Expand Down Expand Up @@ -183,7 +186,7 @@ def bioformats_import(
tiff.imwrite(
tif_dir / upper_row_filename,
image_upper_row,
compression='zlib',
compression="zlib",
photometric="minisblack",
)

Expand All @@ -194,7 +197,7 @@ def bioformats_import(
tif_dir / lower_row_filename,
image_lower_row,
photometric="minisblack",
compression='zlib',
compression="zlib",
)
continue
# for just a simple crop
Expand All @@ -204,12 +207,18 @@ def bioformats_import(
yhi = int(vertical_crop[1] * H)
image_data = image_data[:, ylo:yhi, :]

if horizontal_crop:
nc, H, W = image_data.shape
xlo = int(horizontal_crop[0] * W)
xhi = int(horizontal_crop[1] * W)
image_data = image_data[:, :, xlo:xhi]

tif_filename = f"{file_prefix}_t{t:04d}xy{fov:02d}.tif"
information("Saving %s." % tif_filename)
tiff.imwrite(
tif_dir / tif_filename,
image_data,
compression='zlib',
compression="zlib",
photometric="minisblack",
)

Expand All @@ -220,6 +229,7 @@ def nd2ToTIFF(
image_start: int,
image_end: int,
vertical_crop=None,
horizontal_crop=None,
tworow_crop=None,
fov_list=[],
):
Expand Down Expand Up @@ -291,9 +301,9 @@ def nd2ToTIFF(
# TODO: Make the channel order correct, here and below.
tiff.imwrite(
tif_dir / upper_row_filename,
data = image_upper_row,
data=image_upper_row,
description=metadata_json,
compression='zlib',
compression="zlib",
photometric="minisblack",
)

Expand All @@ -302,27 +312,33 @@ def nd2ToTIFF(
information("Saving %s." % lower_row_filename)
tiff.imwrite(
tif_dir / lower_row_filename,
data = image_lower_row,
data=image_lower_row,
description=metadata_json,
compression='zlib',
compression="zlib",
photometric="minisblack",
)
continue
# for just a simple crop
elif vertical_crop:
nc, H, W = image_data.shape
## convert from xy to row-column coordinates for numpy slicing
yhi = int((1-vertical_crop[0]) * H)
ylo = int((1-vertical_crop[1])*H)
yhi = int((1 - vertical_crop[0]) * H)
ylo = int((1 - vertical_crop[1]) * H)
image_data = image_data[:, ylo:yhi, :]

if horizontal_crop:
nc, H, W = image_data.shape
xlo = int(horizontal_crop[0] * W)
xhi = int(horizontal_crop[1] * W)
image_data = image_data[:, :, xlo:xhi]

tif_filename = f"{file_prefix}_t{t:04d}xy{fov:02d}.tif"
information("Saving %s." % tif_filename)
tiff.imwrite(
tif_dir / tif_filename,
data = image_data,
data=image_data,
description=metadata_json,
compression='zlib',
compression="zlib",
photometric="minisblack",
)

Expand Down Expand Up @@ -374,7 +390,14 @@ def __init__(self):
label="Crop y max", value=1, min=0, max=1, step=0.01
)
self.lower_crop_widget = FloatSpinBox(
label="Crop y min", value=0, min=0, max=0.5, step=0.01
label="Crop y min", value=0, min=0, max=1, step=0.01
)

self.left_crop_widget = FloatSpinBox(
label="Crop x min", value=0, min=0, max=1, step=0.01
)
self.right_crop_widget = FloatSpinBox(
label="Crop x max", value=1, min=0, max=1, step=0.01
)

self.display_nd2_widget = PushButton(text="visualize all FOVs (.nd2 only)")
Expand All @@ -387,15 +410,19 @@ def __init__(self):
self.time_range_widget.changed.connect(self.set_time_range)
self.upper_crop_widget.changed.connect(self.set_upper_crop)
self.lower_crop_widget.changed.connect(self.set_lower_crop)
self.left_crop_widget.changed.connect(self.set_left_crop)
self.right_crop_widget.changed.connect(self.set_right_crop)
self.run_widget.clicked.connect(self.run)
self.display_nd2_widget.clicked.connect(self.render_nd2)

self.append(self.data_path_widget)
self.append(self.exp_dir_widget)
self.append(self.FOVs_range_widget)
self.append(self.time_range_widget)
self.append(self.upper_crop_widget)
self.append(self.lower_crop_widget)
self.append(self.upper_crop_widget)
self.append(self.left_crop_widget)
self.append(self.right_crop_widget)
self.append(self.display_nd2_widget)
self.append(self.run_widget)

Expand All @@ -405,6 +432,8 @@ def __init__(self):
self.set_exp_dir()
self.set_upper_crop()
self.set_lower_crop()
self.set_left_crop()
self.set_right_crop()

napari.current_viewer().window._status_bar._toggle_activity_dock(True)

Expand All @@ -416,6 +445,7 @@ def run(self):
image_start=self.time_range[0] - 1,
image_end=self.time_range[1],
vertical_crop=[self.lower_crop, self.upper_crop],
horizontal_crop=[self.left_crop, self.right_crop],
fov_list=self.fovs,
tworow_crop=None,
)
Expand All @@ -426,7 +456,9 @@ def run(self):
image_start=self.time_range[0] - 1,
image_end=self.time_range[1],
vertical_crop=[self.lower_crop, self.upper_crop],
horizontal_crop=[self.left_crop, self.right_crop],
fov_list=self.fovs,
tworow_crop=None,
)

information("Finished TIFF export")
Expand Down Expand Up @@ -476,8 +508,7 @@ def render_nd2(self):
viewer.add_image(image, channel_axis=1, colormap="gray")
viewer.grid.shape = (-1, 3)
viewer.dims.current_step = (0, 0)
viewer.layers.link_layers() ## allows user to set contrast limits for all FOVs at once

viewer.layers.link_layers() ## allows user to set contrast limits for all FOVs at once

def set_widget_bounds(self):
if self.nd2files_found:
Expand Down Expand Up @@ -522,3 +553,9 @@ def set_upper_crop(self):

def set_lower_crop(self):
self.lower_crop = self.lower_crop_widget.value

def set_left_crop(self):
self.left_crop = self.left_crop_widget.value

def set_right_crop(self):
self.right_crop = self.right_crop_widget.value

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